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calcnoise.py
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calcnoise.py
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#!/usr/bin/env python
import os,sys
import pyfits
from misc import *
from ds9 import ds9
from pyraf import iraf
from optparse import OptionParser
import matplotlib.pyplot as plt
import numpy as np
from scipy.optimize import curve_fit
import math
def gauss(x, *p):
A, mu, sigma = p
return A*np.exp(-(x-mu)**2/(2.0*sigma**2))
def calcnoise(inimg, rap, xmin=None, xmax=None, ymin=None, ymax=None, skywidth=5.0, maxap=500, nhist=30, hz1=None, hz2=None):
# check input image
if not os.access(inimg, os.R_OK):
print >> sys.stderr, 'cannot read input image (%s)' % inimg
return 1
im = pyfits.open(inimg)
im_data = im[0].data
nx = int(im[0].header['NAXIS1'])
ny = int(im[0].header['NAXIS2'])
im.close()
# check range
if xmin == None:
xmin = 1
if xmax == None:
xmax = nx
if ymin == None:
ymin = 1
if ymax == None:
ymax = ny
# check maximum number of apertures
xwidth = xmax - xmin + 1
ywidth = ymax - ymin + 1
buf = int(rap) * 2
x_range = xwidth - 2 * buf
y_range = ywidth - 2 * buf
area = x_range * y_range
apnum = int(area / (rap*rap*math.pi))
if apnum > maxap:
apnum = maxap
# generate randome coordinates
xrand = np.random.rand(apnum) * x_range + (xmin + buf)
yrand = np.random.rand(apnum) * x_range + (xmin + buf)
# calculate flux
flux_arr = []
x = np.ones(im_data.shape[0]*im_data.shape[1]).reshape(im_data.shape[0],im_data.shape[1])* np.arange(im_data.shape[1]) + 1
y = (np.ones(im_data.shape[1]*im_data.shape[0]).reshape(im_data.shape[1],im_data.shape[0]) * np.arange(im_data.shape[0]) + 1).T
for i in range(apnum):
x1 = int(xrand[i] - (buf + skywidth))
x2 = int(xrand[i] + (buf + skywidth))
y1 = int(yrand[i] - (buf + skywidth))
y2 = int(yrand[i] + (buf + skywidth))
im_sub = im_data[y1-1:y2,x1-1:x2]
x_sub = x[y1-1:y2,x1-1:x2]
y_sub = y[y1-1:y2,x1-1:x2]
r = np.sqrt((x_sub-xrand[i])*(x_sub-xrand[i]) + (y_sub-yrand[i])*(y_sub-yrand[i]))
# sky estimation
sky_idx = np.logical_and(r>rap, r<rap + skywidth)
sky = np.median(im_sub[sky_idx])
# encircled flux
phot_idx = np.where(r<=rap)
total_pix = len(im_sub[phot_idx])
flux = np.sum(im_sub[phot_idx]) - total_pix * sky
flux_arr.append(flux)
# histogram
if hz1 == None:
hz1 = min(flux_arr)
if hz2 == None:
hz2 = max(flux_arr)
n, bins = np.histogram(np.array(flux_arr), bins=nhist, range=(hz1,hz2), normed=False, weights=None)
# gaussian fit
bc = (bins[:-1] + bins[1:])/2
p0 = [np.nanmax(n), 0.0, (hz2-hz1)/2.0]
coeff, var_matrix = curve_fit(gauss, bc, n, p0=p0)
n_fit = gauss(bc, *coeff)
sigma = math.fabs(coeff[2])
# plot
plt.ion()
plt.figure()
plt.step(bins[:-1], n, where='post')
plt.plot(bc, n_fit)
plt.xlabel('Aperture flux [ADU/sec]')
plt.ylabel('Number')
plt.title('Radius=%.1f, Nap=%d, Nbin=%d, Sigma=%.2f' % (rap, apnum, nhist, sigma))
plt.grid()
plt.show()
_ = raw_input("Hit enter to finish the script:")
if __name__=="__main__":
usage = "usage: %prog input_image aperture_radius(pix) [options]"
parser = OptionParser(usage)
parser.add_option("--xmin", dest="xmin", type="int", default=None,
help="Minimum X coordinate")
parser.add_option("--xmax", dest="xmax", type="int", default=None,
help="Maximum X coordinate")
parser.add_option("--ymin", dest="ymin", type="int", default=None,
help="Minimum Y coordinate")
parser.add_option("--ymax", dest="ymax", type="int", default=None,
help="Maximum Y coordinate")
parser.add_option("--skywidth", dest="skywidth", type="int", default=5,
help="Width of sky annulus in pix (default=5)")
parser.add_option("--maxap", dest="maxap", type="int", default=500,
help="Maximum number of apertures (default=500)")
parser.add_option("--nhist", dest="nhist", type="int", default=30,
help="Number of bins in the histogram (default=30)")
parser.add_option("--hz1", dest="hz1", type="float", default=None,
help="Minimum bin value in the histogram")
parser.add_option("--hz2", dest="hz2", type="float", default=None,
help="Maximum bin value in the histogram")
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_help()
sys.exit()
calcnoise(args[0], float(args[1]), xmin=options.xmin, xmax=options.xmax, ymin=options.ymin, ymax=options.ymax, skywidth=options.skywidth, maxap=options.maxap, nhist=options.nhist, hz1=options.hz1, hz2=options.hz2)